Variant report

Variant	rs2066594
Chromosome Location	chr13:50721497-50721498
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50719538..50722046-chr13:50723556..50725179,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1326120	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2066549	0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2066558	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2066572	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2066575	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2066585	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2066587	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2066591	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2242482	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2687951	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2740508	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2740544	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2740545	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2760914	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2803839	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2812204	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2812216	0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2812217	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2812222	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2997624	0.85[AMR][1000 genomes]
rs4942899	0.81[AMR][1000 genomes]
rs4942901	0.94[AMR][1000 genomes]
rs7338055	0.81[AMR][1000 genomes]
rs9568363	0.91[AMR][1000 genomes]
rs9568364	0.91[AMR][1000 genomes]
rs9596215	0.89[AMR][1000 genomes]
rs9596219	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9596220	0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv832608	chr13:50678628-50888413	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv1041501	chr13:50683189-50795195	Flanking Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	nsv900076	chr13:50710579-50912578	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2066594	DLEU2	Cis_1M	lymphoblastoid	RTeQTL
rs2066594	DLEU2///DLEU2L	trans	lymphoblastoid	RTeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50715600-50726400	Weak transcription	Brain Cingulate Gyrus	brain
2	chr13:50716000-50723200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr13:50716000-50723600	Weak transcription	HUES6 Cell Line	embryonic stem cell
4	chr13:50716200-50723600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr13:50718400-50727800	Weak transcription	Stomach Mucosa	stomach
6	chr13:50718800-50723600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr13:50719000-50725600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr13:50719200-50723400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr13:50719200-50723600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:50719200-50723800	Weak transcription	Brain Germinal Matrix	brain
11	chr13:50719200-50724200	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr13:50719200-50726000	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr13:50719200-50726200	Weak transcription	Primary B cells from peripheral blood	blood
14	chr13:50719400-50723400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr13:50719400-50723400	Weak transcription	NHDF-Ad	bronchial
16	chr13:50719400-50726400	Weak transcription	Brain Hippocampus Middle	brain
17	chr13:50720000-50723200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr13:50720800-50721800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr13:50721000-50722000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr13:50721200-50726600	Weak transcription	HepG2	liver
21	chr13:50721400-50726000	Weak transcription	Osteobl	bone

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